Merge branch 'main' of github.com:JohriLab/Bvalcalc

Author: jacobimarsh

docs/source/guides/demography.rst

@@ -3,7 +3,7 @@ Demographic Inference with B-map
 
 Demographic inference is confounded by the linked effects of selection; see `Johri et al. (2021) <https://doi.org/10.1093/molbev/msab050>`_ for biases in MSMC-like and SFS-based approaches, and `Marsh and Johri. (2024) <https://doi.org/10.1093/molbev/msae118>`_ for biases in ARG-based approaches.
 
-To best avoid biases, it is essential to only use the most neutrally-evolving sites for demographic inference , i.e. the sites least affected by sweeps and BGS (highest B). 
+To avoid biases, it is essential to only use the most neutrally-evolving sites for demographic inference , i.e. the sites least affected by sweeps and BGS (highest B). 
 
 Using ``--Bmap`` (see :doc:`B-map Utilities for VCF <../modules/bmap_utils>`), we can use a B-map from ``--genome`` to filter a VCF or CSV to keep only the most neutrally evolving sites.
 
@@ -49,4 +49,4 @@ Using the newly saved `filtered_positions.csv` and our original VCF we can filte
         -R variants_B_above_0.9.txt \
         your.vcf -Ov -o filtered.vcf
 
-Now the `filtered.vcf` only contains sites with B >= 0.9 and is ready for more accurate demographic inference with your tool of choice!
+Now the `filtered.vcf` only contains sites with B >= 0.9 and is ready for more accurate demographic inference with your tool of choice!